Fulfilling the Missing Puzzle Pieces of Arhodomonas sp. Seminole by DNA Sequencing, PCR Distribution, and Gel Electrophoresis

Abstract

Arhodomonas sp. Seminole was an aerobic halophilic bacterium that was isolated and enriched from an oil-site in Seminole County here in Oklahoma. Enrichment was performed by starting with a simple soil sample that was placed in a liquid media with high –salt minerals and various aromatic hydrocarbons which grew at room temperature. A small amount would be transferred numerous times to the fresh media that contained the salt. The product of the enrichment was the bacterium of Arhodomonas sp. Seminole: a salt-loving, aromatic hydrocarbon-metabolizing bacterial. This bacterium required salt and grew on a wide variety of carbon sources: lactate was found to be the best carbon source. Since the bacterium was halophilic, salt was a very important requirement in order for this bacterium to prosper. The abilities of Ahrodomonas sp. Seminole were to metabolize benzene, toluene, phenol, 4-hydroxybenzoic (4-HBA), protocatechuis acid (PCA), 12, and phenylacetic acid (PAA) as the sole sources of carbon at a very high salinity. Ahrodomonas was sequenced. However, this led to a problem. Instead of the complete genome of Arhodomonas being one single, contiguous piece of DNA, it was a 750-contig piece of DNA which made the genome incomplete. Our mission was to conclude if our two given contigs were side-by-side on the same chromosome with a small gap in between them by using a reference protein along with a fused contig. From the results, we were able to conclude if our contigs were alongside each other, if there was a gap, and if our fused contig resembled an actual known protein.